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Structure of human trkb receptor ligand binding domain in complex with the Fab frgment of antibody AB20
Analyse Structure of human trkb receptor ligand binding domain in complex with the Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MO9
- Type
- protein
- Length
- 533 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AB20 Fab heavy chain; AB20 Fab light chain; BDNF/NT-3 growth factors receptor
- EC
- 2.7.10.1
- UniProt
- Q16620
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | AB20 Fab heavy chain | protein | 212 | 6% helix, 54% strand | — |
| L | AB20 Fab light chain | protein | 219 | 5% helix, 51% strand | — |
| X | BDNF/NT-3 growth factors receptor (EC 2.7.10.1) | protein | 102 | 3% helix, 59% strand | Q16620 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.52 | 0.75 | 43 | empty |
| 2 | 356 | 0.51 | 0.72 | 47 | empty |
| 3 | 129 | 0.40 | 0.74 | 27 | empty |
| 4 | 69 | 0.31 | 0.74 | 15 | empty |
| 5 | 67 | 0.30 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1716 Ų buried · 10 hydrogen bonds · protein-protein
- H–X · 487 Ų buried · 5 hydrogen bonds · protein-protein
- L–X · 414 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5MO9 · Structure of human TrkB receptor ligand binding domain in complex with the Fab frgment of… · the same entry in another collection · chain H against H, TM-score 1.00
- Q16620 · AlphaFold monomer V2.0 prediction for BDNF/NT-3 growth factors receptor (Q16620) · a predicted model of the same protein · chain X against A, TM-score 0.91
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q16620
- Elsewhere: RCSB PDB 5MO9 · PDBe 5MO9 · UniProt Q16620
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